The July 2007 mouse (Mus musculus) genome data were obtained from the Build 37 assembly by NCBI and the Mouse Genome Sequencing Consortium. For more information about this assembly, see MGSCv37 in the NCBI Assembly database.

Exotome Browser

We have ablated the cellular RNA degradation machinery in differentiated B cells and pluripotent embryonic stem (ES) cells by conditional mutagenesis of core (Exosc3) and nuclear RNase (Exosc10) components of RNA exosome and identified a vast number of novel long non-coding RNAs (lncRNAs) and enhancer RNAs (eRNAs). Unexpectedly, eRNA-expressing regions accumulate R-loop structures upon RNA exosome ablation, thus demonstrating the role of RNA exosome in resolving deleterious DNA/RNA hybrids arising from active enhancers. We propose RNA exosome simultaneously protects divergently transcribed enhancers, by resolving deleterious transcription-coupled secondary DNA structures, while also regulating long-range super-enhancer chromosomal interactions important for cellular function.

Noncoding RNA transcription targets AID to divergently transcribed loci in B cells.
Evangelos Pefanis*, Jiguang Wang *, Gerson Rothschild*, Junghyun Lim, Jaime Chao, Raul Rabadan^# , Aris N. Economides, Uttiya Basu^#.
Nature 2014 Oct 16;514(7522):389-93. doi: 10.1038/nature13580.

RNA-Exosome-Regulated Long Non-coding RNA Transcription Controls Super-Enhancer Activity.
Evangelos Pefanis*, Jiguang Wang*, Gerson Rothschild*, Junghyun Lim*, Kazadi D, Sun J, Federation A, Chao J, Elliott O, Liu ZP, Economides AN, Bradner JE, Rabadan R^#, Basu U^#.
Cell 2015 May; doi: 10.1016/j.cell.2015.04.034.

*These authors have contributed equally to this work. ^#Corresponding authors.